GNE myopathy (also known as hereditary inclusion body myopathy (HIBM)) is an adult-onset muscle disorder characterized by impaired sialylation of (muscle) glycans, detectable by lectin histochemistry. This article describes a standardized method to quantify (lectin-)fluorescence in muscle sections, applicable for diagnosis and response to therapy for GNE myopathy. The results show that Sambucus nigra agglutinin (SNA) fluorescence co-localizing with CAV-3 was ∼50% decreased in GNE myopathy biopsies compared to muscle-matched controls, confirming previous qualitative results. The autgors conclude that this quantitative fluorescence method can accurately determine sialylation status of GNE myopathy muscle biopsies.